Running Zigbee2MQTT alongside Home Assistant on the same device may seem convenient, but it often leads to issues like devices disappearing or failing to restart after a reboot. Separating Zigbee2MQTT into its own dedicated device can solve these problems.
Zigbee2MQTT’s main challenge is that when your host device reboots, so does Zigbee2MQTT. This means that if you’re running it alongside Home Assistant on the same device, your Zigbee network will also go down during a reboot.
However, this isn’t always the end of the world. In many cases, things recover within minutes after Home Assistant and Zigbee2MQTT start up again. But there are instances where issues persist even with Zigbee2MQTT set to start on boot.
Some users have reported problems when their host reboots, resulting in Zigbee devices disappearing from Home Assistant. This makes it difficult to diagnose the issue.
Separating Zigbee2MQTT into its own device solves these problems by making troubleshooting easier. If your Zigbee devices drop off, you can now pinpoint whether the issue lies with Home Assistant or Zigbee2MQTT itself.
Moreover, running Zigbee2MQTT on a separate device means you can reboot your Home Assistant server without affecting it, and vice versa. This also allows for optimal placement of the coordinator to ensure better connectivity throughout your home.
Another advantage is that it removes USB passthrough issues common when running Home Assistant in a virtual machine or container. By having Zigbee2MQTT on its own device, you can bypass these problems and keep your network stable.
Source: https://www.howtogeek.com/zigbee2mqtt-is-the-weakest-link-on-your-home-assistant-server